My humble two cents:
1) Always thoroughly dish-soap (non-scented) and rinse my bottles out after drinking
2) On the day before bottling, I run the bottles through the dishwasher, no detergent
3) Morning of bottling day: since I always have a simple spray-bottle w/StarSan solution handy, I upside-down spray into the bottles; 4 quick pumps as I slightly swirl each bottle. A quick upside down shake to evenly distribute and shed excess foam, then back into the bottle case, done. I can methodically pound out 48 bottles in under 10 minutes this way, music playing and me humming along.
Being consistent with this method, I never spend too much time at any one point working on cleaning/sanitizing bottles (5-10 min work-time, at most, for each of the above steps), and have thus far avoided the "bottling-as-major-headache" thing.
Hope it's going well for you!
EC